[gmx-users] Replica exchange simulations more than number of processor

[Christopher Neale]

What I have is only my own personal unpublished data. But add to that the number of years since REST2 came out and the low number of papers in which anybody did something useful with it and I'd say that suggests many others have tried and run into the same issues that I did (or maybe I'm just not reading the right papers, so please correct me if I am wrong). When my desired use failed I fell back to trp-cage folding in water and found the same things, so it's not like REST2 only fails for some exotic systems. Running 3 entirely separate repeats of regular T-REMD and 3 of REST2, I found that overall T-REMD is of similar or perhaps better efficiency (even though it has more replicas) compared to REST2. It's an on/off area of research for me, attempting to fix REST, but I still don't have a good answer for it.


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Szilárd Páll <pall.szilard at gmail.com>
Sent: 14 April 2017 12:26:41
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replica exchange simulations more than number of       processor

On Fri, Apr 14, 2017 at 5:51 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> Just my 2 cents: REST2 doesn't work. The random walk is much better than
> REST but the sampling efficiency at low lambda is now poor.


Interesting. Is there any (published) data you could point to that supports
this?


> Your mileage may vary, but be aware that REST2 is not necessarily going to
> be useful for all systems.
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Thomas
> Piggot <t.piggot at soton.ac.uk>
> Sent: 14 April 2017 09:23:35
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Replica exchange simulations more than number of
> processor
>
> In addition, using another technique like REST2 may substantially reduce
> the numbers of replica's you need. Still, more compute is definitely
> recommended if you can get it.
>
> Cheers
>
> Tom
>
> On 14/04/17 12:48, Smith, Micholas D. wrote:
> > You can try over assignment of cores, but that will be horribly slow. Or
> use more than 1 node (if you can get it).
> >
> > ===================
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Мижээ
> Батсайхан <b.mijiddorj at gmail.com>
> > Sent: Friday, April 14, 2017 4:16 AM
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Replica exchange simulations more than number of
>  processor
> >
> > Dear gmx users,
> >
> > I would like to simulate folding of a peptides. I have only 12 core
> > processor, and I assumed the number of replica using temperature
> generator
> > as following link
> > http://folding.bmc.uu.se/remd/.
> >
> > The number of replica is about 60. How can I solve this problem? Can you
> > advice me, please?
> >
> > Best regards,
> > Mijee
> > --
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> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
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